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This page was generated on 2022-12-02 11:10:39 -0500 (Fri, 02 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4210
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4122
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4188
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for VariantAnnotation on merida1


To the developers/maintainers of the VariantAnnotation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2106/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.45.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-12-01 14:00:17 -0500 (Thu, 01 Dec 2022)
git_url: https://git.bioconductor.org/packages/VariantAnnotation
git_branch: master
git_last_commit: 3fc786d
git_last_commit_date: 2022-11-01 11:06:07 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'Rsamtools' which is not available

Summary

Package: VariantAnnotation
Version: 1.45.0
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.45.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir
StartedAt: 2022-12-02 10:19:25 -0500 (Fri, 02 Dec 2022)
EndedAt: 2022-12-02 10:22:25 -0500 (Fri, 02 Dec 2022)
EllapsedTime: 179.7 seconds
RetCode: 0
Status:   OK  
PackageFile: VariantAnnotation_1.45.0.tgz
PackageFileSize: 3.969 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.45.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.45.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantAnnotation’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c dna_hash.c -o dna_hash.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rle.c -o rle.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c strhash.c -o strhash.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c utilities.c -o utilities.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vcffile.c -o vcffile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vcftype.c -o vcftype.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c writevcf.c -o writevcf.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VariantAnnotation)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so"